By Your Side
by PotterheadWhovian7
Summary: John and Sherlock are back together after the Fall. They are a couple- finally- and are facing the challenges of life as it goes on. But their comfortable life is interrupted by kidnappings of Sherlock's friends. Who is doing this? Will John be next? How will Sherlock deal with leaving the most important thing in his life? Sequel to Nothing Is Impossible. CAN be read alone!
1. Chapter 1

"Good morning, Sherlock," John sighed, walking into the sitting room with a cup of tea in his hand. He was dressed in a pea green dressing gown and had his pajamas on underneath.

He sat next to Sherlock on the sofa and curled up next to him. He rested his head on Sherlock's shoulder and pulled up his knees. Sherlock wrapped his free arm around John as he read the paper. He kissed the top of John's sandy hair and mumbled a "Good morning," in return.

They sat there for a few minutes, reading about a recent murder that took place in another country. Sherlock sighed and put the paper down.

"It was the sister," he said. "Obvious. In the background of the security camera picture, you can see a shadow that's holding a..." he rambled, and after a while, John stopped listening.

He though about how lucky he was to have a boyfriend like Sherlock. He left body parts in the refrigerator, true, and conducted lethal experiments on the kitchen table, but at least he was smart, funny (when he wanted to be), had an interesting life that John shared, and, John had to admit, he was a damn good kisser.

Three years ago, Sherlock had faked his death, leaving John alone and broken. However, a few months ago, Sherlock had returned, and just a short while ago (on New Year's Eve), they had become a couple.

When Sherlock stopped talking, John announced that he would make breakfast. He made them both an omelet, then sat next to Sherlock again. He leaned against his flatmate and placed his head on Sherlock's shoulder again. Sherlock laid his head on top of John's, and they stayed like that for a long time.

After they both finished eating, Sherlock turned to John and captured his lips. John sighed in happiness- he had been hoping for this- and wrapped his arms around Sherlock. He tilted his head for the ideal kissing angle and opened his mouth, letting Sherlock's tongue find its way into John's mouth.

With a moan, John moved closer to Sherlock. He was practically sitting on top of Sherlock now, and he slid his hand through the collar of Sherlock's shirt, trailing his hands over the other man's chest.

"I love you, you know that?" John moaned as Sherlock kissed and sucked at John's neck, right where his pulse was. It was beating hard and fast.

Sherlock groaned in response and clutched at the back of John's shirt. He pulled John over him, so that the ex-army doctor was straddling the detective. He lay back against the arm of the sofa and brought his lips towards John's once again.

Half an hour later, John pulled away finally. His dressing gown was off and thrown across the room, while his pyjama shirt was half unbuttoned.

He retrieved his robe and pecked Sherlock on the cheek, before heading towards his room to change into clothes for the day.

OoOoOoO

Somewhere in the many twisted and cloudy streets of London, Greg Lestrade walked down the street, texting on his phone. Suddenly, a hand came out from the alley and grabbed his neck, pulling him into the darkened alley.


	2. Chapter 2

**Chapter 2**

_Previously..._

_Somewhere in the many twisted and cloudy streets of London, Greg Lestrade walked down the street, texting on his phone. Suddenly, a hand came out from the alley and grabbed his neck, pulling him into the darkened alley._

OoOoOo _Now_ OoOoOo

Yells and screams of pain echoed around an abandoned warehouse countries away from 221B. It was a dark, cold, wet place full of the terrors that should stay in nightmares.

A man lay in the center of the maze that made up the corridors of the warehouse. His ID would say his name was Greg Lestrade, although he didn't look it at the moment.

His face was swelled up and bruised, with cuts and scrapes running down his neck. His arms could tell tales of whips and burning metals. The rest of his body wasn't much better- he scarcely had the energy to breathe.

As the darkness threatened to consume him, Greg Lestrade silently prayed to any God listening.

Please... just make it stop.

OoOoOoO

Back in London, Sherlock Holmes was lying on the sofa, his hands folded beneath his chin. He was watching John clean the kitchen with a small frown upon his face. Something was wrong... he could feel it...

He jolted up as someone knocked on the door.

"Come in," Sherlock said as John emerged from the kitchen.

A man in a black suit walked in. He had dark hair that was just starting to turn grey. Sherlock quickly deduced that he was previously married, but recently divorced. The marriage was happy until just recently. He had one big dog and worked both inside and outdoors.

"What do you want?" Sherlock asked sharply. John was beside Sherlock, and glanced at his partner as if to say 'Calm down, Sherlock. Let the man talk'.

"Good to see you, too. My name is Athenly Jones, detective for Scotland Yard. I'm afraid I have some bad news about my colleague, Mr. Lestrade."

"Oh, please sit down," John offered, gesturing to a chair.

"Thank you, Dr. Watson. I'll get right to the point. Mr. Lestrade was walking home from work last night, apparently. Nice weather for once. He didn't arrive home, according to his wife. She informed us this morning. He has not shown up on any CCTV footage between here and his flat."

John and Sherlock stood there in front of Mr. Jones, completely surprised. Sherlock reacted first as his phone vibrated.

_I just got the news, also. I'll check my cameras. -Mycroft_

Sherlock breathed a small smile of relief before turning back to the other two. "Thank you for the visit, Mr. Jones. I hope to never see you again," Sherlock said politely with the smile he used only for the normal people.

Athenly Jones looked affronted. "I- well- Goodbye, then," he replied as Sherlock shoved out of the door.

"What was that?" John asked, pointing towards the phone.

"Mycroft. If anyone has the power to pry into every corner of the country, it's my sorry excuse for a brother," Sherlock replied snappily, before curling up on the sofa, his brain already ransacking his Mind Palace for a suspect.

John and Sherlock spent the day in 221B, waiting for more news. None came, however, until John had already gone to bed.

Sherlock got a call around midnight. Frowning at the "Blocked Number", the detective answered the call cautiously. "Hello? Who is this?"

"That... does not... matter," a familiar, tired voice replied. "I will... find you... and kill you."

Sherlock frowned deeper. "Lestrade? Is that you?"

"Greg... is my voice. I am... pointing a gun... to his head."

"What do you want?"

"You. You, Sherlock Holmes, will die." With that, Lestrade (or the person holding him captive) hung up.

Sherlock didn't tell John or the police. He didn't think it was necessary. Why scare anyone? He didn't get any calls again. Nobody mugged him on the street. Sherlock almost deleted it, but kept it incase it became useful later. Honestly, he wasn't to worried about Lestrade. Greg was a strong man.

He could last.

Right?


	3. Chapter 3

**A/N:** **Hey, so I know it's been more than a month, but on the the bright side, I got a beta- the wonderful Zylstra- so chapter will show up faster and better. Onwards!**

Molly Hooper had been taken.

She had been alone in her apartment, and she didn't show up for work the next day. When people called her cell and she didn't answer, some people for Bart's went over there after their shift ended. Her door was open and some blood was found on the floor. Her cat, Toby, was laying on the couch with signs of someone else's blood on his claws (none of testing came up with a match for that blood). Scotland Yard was called in, and Jones investigated. There were various signs of struggle, but no one was in the flat.

That afternoon, Jones texted Sherlock, telling him all of this information.

This all made John worry. As his boyfriend sat on the sofa, lost in the depths of his mind palace, John drank cup after cup of tea, trying to connect the dots.

Moriarty was dead. Sherlock had taken down all of the professor's web. Who did that leave?

Well, really, any criminal in London. The only problem was that all of these kidnappings seemed to be centered around Sherlock and him. Irene Adler was either in America or dead, as far as he knew, and she didn't seem the type to do all of this.

So that meant unless Moriarty came back from the dead like Sherlock, it was just a common criminal on the streets, and the connection between the two people was a coincidence.

However, Scotland Yard was starting to have suspicions. None of them fully trusted Sherlock, and it did not help that he had faked his death.

OoOoOoO

John was going through Molly's blog. she seemed kind of lonely most of the time. Molly talked a lot about her cat and 'Jim'. John silently cursed the dead man for tricking Molly in such a cruel way. She really was a sweet woman. John wished he knew her better. Maybe he would invite her over for tea if they ever found her.

When? Or if?


	4. Chapter 4

Anthea, Mycroft's assistant, walked into her boss's large office. She was holding the cup of tea he had asked for just minutes earlier. However, no one was behind the wooden desk to drink it. Instead, papers had been thrown all over the place and Mycroft was gone.

She drew in a deep breath. She was good friends with her boss, and she had never been in a situation like this before. Fighting back the panic that threatened to consume her heart, she quickly dialed 911.

Anthea was redirected to an Inspector Jones, who was working other disappearance cases.

"Hello?" he asked, "What's the emergency?"

"Um, hi, sir. I just walked into my boss' office, and he's gone. Mycroft was here just a second ago, I swear!" Anthea answered, he voice slightly shaky.

"Alright, ma'am. What was his full name?"

"Holmes. Mycroft Holmes. He works for the government..." Anthea trailed off as she heard a deep sigh come from the other end of the phone. "What? Whst is it?"

"We've been getting a lot of kidnappings lately, is all. They all seem connected to this Sherlock Holmes bloke. Besides that, there's no clues, no motives. To be honest, we just don't know what to do."

After that, they quickly wrapped up their conversation, and Jones and his men were brought in.

Mycroft's kidnapping was classified officially as connected with Lestrade's and Molly's.

OoOoOoO

Back at 221B, Sherlock was sleeping. He hadn't slept for about a week, so John made him finally lay down on the sofa and close his eyes. He had been asleep for about two hours before his phone rang.

"Hello?" Sherlock asked, his voice groggy, rubbing sleep out of his eyes.

"Hello, Mr. Holmes. It's Jones. Did you hear about the third kidnapping?"

"What? No, I didn't. Who was it this time?"

Jones sighed. "It was... Mycroft. Sherlock, I'm going to have to-"

Sherlock, however, hung up. He lay back on the sofa and sighed deeply.

At that moment, John walked in. "What happened? I heard voices."

"Jones called," Sherlock droned in his deep voice.

John looked confused. "Why?"

"Mycroft was taken."

Realization spread over John's face. He knew Sherlock and Mycroft weren't on the best of terms, but they were still brothers who cared for each other in their weird, messed up way.

John also knew that Sherlock being Sherlock, he would try and squash all of his feelings instead of dealing with them.

OoOoOoO

Everyone at Scotland Yard was in a frenzy. Not only was one of their detectives gone, but the other disappearances seemed to leave no clues at all.

Everyone who knew about the case suspected Sherlock. The evidence- or lack thereof- seemed to point nowhere else.

No one wanted to call Sherlock in. Because of the lack of clues, they could not arrest him. The question was: why was he taking the people closest to him? None of it made any sense.

OoOoOoO

"What... do you want... from me?" Mycroft rasped out, blood trickling down his chapped lips.

He was kneeling on the ground on both of his knees. His hands were tied behind his back in chains. Already, even though he had been in that place for much less than a day, his clothes were torn and every muscle in his broken body ached.

"Oh, nothing from you," a cold, laughing voice replied. "You're just the bait." A figure stepped into the light streaming through the small window. Mycroft's eyes widened as he laid eyes on the hard, unforgiving face of James Moriarty.


	5. Chapter 5

**A/N: See? I told you guys I would be faster :P**

**Alright, school's really busy right now (I'm not kidding- I had to finish three projects over the weekend), but I'll try to get the next chapter to you guys ASAP.**

**Thanks to Zylstra for beta-ing this! Onwards!**

The night after Mycroft was taken, Sherlock awoke abruptly to the sound of a loud thump and muffled scream. He jumped up and ran down the stairs, almost toppling over John. They both ran down the main stairs and into Mrs. Hudson's flat.

A small pool of blood lay on the floor and the door was wide open. Mrs. Hudson was nowhere in sight.

Sherlock immediately began to deduce the scene. He could just barely smell the sweet scent of chloroform.

Sherlock glanced over to see what John was doing. He had dipped a finger in the blood. It was obviously fresh and Mrs. Hudson's. Sherlock groaned and rushed out of the room, pinching the bridge of his nose. John trailed behind him.

How could he be so stupid? They were targeting closer and closer to home, of course they would break in. How could he have missed something so obvious? He should have kept awake, he should have been alert, he should have... should have...

"Sherlock? Sherlock, I need you to calm down." John's voice broke through Sherlock's frantic thoughts. A phone was in John's hand, and he had already called Scotland Yard.

They waited together as the police made their way over. Sherlock seemed to be freaking out more than he should be. He was breathing was faster than normal, and his eyes glistened. To John, it was a sudden reminder of the case in Baskerville.

"Sherlock, I seriously need you to stop. Breathe in and out. There we go..." John said to Sherlock, rubbing his back soothingly. He sat them down on the stairs as the adrenaline started to wear off. Sherlock closed his eyes and leaned his head against John's shoulder. The detective let out a deep sigh and wrapped his arm around John's waist.

"What's wrong, Sherlock? Why are you acting like this?" John asked, burying his nose in Sherlock's dark hair.

"This all just reminds me of the Reichenbach situation," Sherlock murmured. And it did have its parallels; everyone close to him was being threatened, and there seemed no way out.

After Sherlock 'died,' he had gone through a lot in the three years he was gone. Hunting down the best snipers in the world was not very easy.

He had gathered a notable collection of scars that he would never explain.

All of this- the kidnappings, threatenings, even the phone call- all were such a bitter reminder of Moriarty. He and John couldn't go through that again...

In a few minutes, the police had arrived and red and blue lights flashed off the surrounding buildings. Faces peered out of nearby windows, trying to get a glimpse at what was going on.

Jones approached them, and Sherlock caught a glimpse of John's relieved face.

"Mr. Holmes, I'm afraid I'm going to have to send you and Dr. Watson away," Jones said, and John's face fell.

"Away? Why? Where?" Sherlock asked, his mind still reeling. What if the kidnapper came for him next? Or worse, John? Nothing was adding up. It had to be Moriarty, and yet it couldn't be...

Jones was now saying something about a safe house.

"...So you and Dr. Watson will be unable to be found in the event of another

kidnapping," he concluded.

John frowned deeply. "Are Sherlock and I allowed to stay in the same house?"

"Unfortunately, we are going to have to split you up, for further security."

"What? No. Nope, I'm not leaving John," Sherlock hissed icily, glaring at Jones.

"I am sorry, Mr. Holmes. I'll give you two a few moments," with that, he walked away into the crowd of frantic police officers running around.

Sherlock turned towards John, who was licking his lips nervously. "We-we'll be fine, Sherlock. A-and it won't be long before they catch this guy... " John trailed off. They wouldn't have a chance to solve the case after they were separated.

Sherlock pulled John into a tight embrace. He felt John bury his face into Sherlock's shoulder and shake with silent sobs.

When they pulled back, Sherlock brought their lips together. He moved his mouth rhythmically against John's and closed his eyes. The detective poured all of his love for John into that simple display of affection. He didn't know when he would be able to see his lover again, or what would happen while they were separated.

When they pulled back, Sherlock let out a long sigh. "I, um, I'll see you."

He could already see police officers coming over.

They were put in separate police cars. Sherlock leaned his head against the window as he watched the scenery fly by. How had all of this happened so fast?

OoOoOoO

John was walking back to his house from his weekly trip to the grocery store. Luckily, their chip and PIN machines actually work. As he walked, he noticed that all of the houses in his neighborhood looked the same. Every house had the same white fence, green lawn, and they even seemed to all have the same curtains.

Oh, how he missed the unique streets of London.

John's safe house wasn't too bad, as far as safe houses go. It looked like all of the other houses from the outside, but inside it had a state-of-the-art alarm system, steel-plated doors, and even a concrete panic room in the basement. When he was a kid obsessed with spy shows, he would have loved it.

But, however cool it might seem, living in a safe house was really boring. John wasn't allowed to go outside much, so he quickly ran out of things to distract him from the aching in his chest. He missed Sherlock so much.


	6. Chapter 6

John was incredibly bored.

He now knew why Sherlock took up shooting the wall. Anything to break this insufferable silence, to cause a bit of commotion. He had only been at the safe house about a week, but was already he would murder someone if he could get him and Sherlock back together, solving cases.

Thinking of Sherlock hurt, though. John was always expecting to turn the corner and see him there, hands folded under his chin in a thoughtful pose. He missed Sherlock with all of his heart. The thing he wanted most in this world was to return home, to 221B, and relax with his boyfriend.

OoOoOoO

Sherlock wasn't dealing with the separation well, either. He had practically snarled at a police officer who came to see if he was okay.

He and John weren't allowed to contact each other in any way. No calling, emailing, or texting. The detective hardly ate, and scarcely slept. He spent most of his time in his Mind Palace, sorting through his John files. Sherlock seemed incapable to delete anything that had to do with John. Every little thing was precious, like when they sat on the sofa kissing, or even when John badgered Sherlock to get the milk for once.

As the detective lay on his sofa day after day, he became thinner and thinner. His eyes sunk into his head and his skin became waxy after so long without eating.

OoOoOoO

About a week and a half after Sherlock and John had been moved to safe houses, Sherlock received a text from an unknown number. Deeming this a reasonable distraction, Sherlock opened it.

Inside were pictures of Lestrade, Mycroft, and Molly. Lestrade seemed to be the worst of them. All three were tied up in some sort of basement, obviously tortured and starved. Lestrade was in the most pictures, looking gruesome covered in blood and wearing the same clothes he disappeared in. At least one of his arms were broken and, judging from his posture, so were quite a few ribs.

The text also contained some words.

_Your pet Johnny is next. -JM_

Sherlock drew a sharp breath. Not John. He had to keep John safe, never let him out of his sight-

But then the detective remembered. He'd already let John out of his sight. Quickly forwarding the message to Jones, Sherlock receded back into his mind, shutting himself off from the world, ignoring the rumbling of his empty stomach.

How would the world go on if John was taken? How would Sherlock survive?

He was well and truly alone without his John.


	7. Chapter 7

As John stood at the door of his safe house, the bag of groceries dropped from his hand. All the furniture and objects in the house were strewn everywhere- books were littering the room, sofas were overturned, and the curtains were ripped.

A large man dressed all in black – including a ski mask over his face – sat calmly on an upturned table.

"Hello, Dr. Watson," the man said in a high voice. He was obviously changing how he sounded. "I have a message for you from Professor Moriarty. He says, 'I'll be seeing you soon.'"

With that, the man lunged towards John, and the doctor felt something hit his head as blackness overtook his vision.

OoOoOoO

As soon as John woke up, he called the police. Taking a deep breath to steady himself, he sat down on the sofa and pinched the bridge of his nose. How had this happened? He hadn't been gone for that long, and this house was made to prevent something like this.

When the police pulled up outside, sirens blaring, John stood up, wiping his sweaty palms on his jeans and walking outside to meet them.

A special team had come out, because he was under a protection program. A nice woman questioned him while the rest went over the scene with a fine-toothed comb. Then, they all walked through the house, trying to see if anything was missing. As far as John could tell, nothing was.

John was sent to another safe house as a precaution. It was in a much more rural area, and was a bigger house. It smelled of fresh paint and carpet shampoo, and looked, for all its security, like a normal house. But it wasn't home.

John felt _terrible_. He was jumpy and didn't want to leave the house. John barely ate, and got little to no sleep. John's heart always seemed to be pounding in his ears. He couldn't stop thinking about what the man had said. Moriarty would be 'seeing him soon.' John didn't want to have to be protected, he didn't want to be kidnapped, and, most of all, he didn't want to be _lonely_ anymore.

John sighed and laid his head in his hands, tangling his short hair through his fingers.

He'd never been so afraid in his life.


End file.
